git.txt

Notes on git

Initial stuff

  git config --global user.name "Your Actual Name"
  git config --global user.email "youremail@somewhere.com"

  git config --global color.diff auto
  git config --global color.status auto
  git config --global color.branch auto

  git config --global core.editor emacs

  git config --global core.excludesfile ~/.gitignore_global

Clone repository

  git clone git@github.com:kbroman/qtl
  git clone git://github.com/kbroman/qtl
  git clone https://github.com/kbroman/qtl

The basics

  git pull
  git commit -a
  git push

Also

  git status
  git diff
  git diff 1.16-6 R/est.map.R
  git diff 1.16-6 R/est.map.R | gitx
  git diff --name-status main..[some branch]

Tagging

  git tag -a -m "tagging version 1.11-7" 1.11-7
  git push --tags
  git tag -d 1.11-7                     [deleting a tag]
  git push origin :refs/tags/1.11-7     [remove tag from origin that I'd removed locally]
  git push --delete origin 1.11-7       [another way to remove tag from origin]
  git tag -a tag_label 9fceb02 -m "Message here"  [tag an older commit]

Branching and merging

  git branch                            [to see what branches there are]
  git branch blah                       [to create the 'blah' branch]
  git checkout blah                     [to switch to the 'blah' branch
  git checkout main; git merge blah   [merge blah into main]


Going back

  git reset --hard                      [throw all changes away]
  git checkout myfile.txt               [throw away changes to myfile.txt]
  git commit --amend                    [revise the last commit message]


github stuff

  git checkout MQM
  git pull git@github.com:myfriend/rqtl-mqm.git
  git pull git@github.com:myfriend/rqtl-mqm.git/main

  git pull myfriend main
  git pull myfriend myfriend

  git push --set-upstream origin <branch>
  git push origin <branch>
  git push origin --delete <branch>

  git remote prune origin --dry-run  # Check for defunct remote branches
  git remote prune origin            # Delete local copies of defunct remote branches


To remove a local copy of a remote branch (say it shows up in
"branch -a" as "remotes/origin/pptx

  git branch -r -d origin/pptx


github remotes; see https://docs.github.com/en/get-started/getting-started-with-git/managing-remote-repositories

 git remote add myfriend git://github.com/myfriend/qtlHD.git

 In .git/config:
    [remote "myfriend"]
    url = git://github.com/myfriendp/qtlHD.git
    fetch = +refs/heads/*:refs/remotes/myfriend/*

After pulling from origin, use the following to get access to a branch
only on origin:

  git checkout -b mybranch origin/mybranch


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Searching github:

   https://github.com/search?utf8=%E2%9C%93&q=session_info+filename%3A.travis.yml

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bitbucket:  Had trouble with ssh; here's what seemed to work

  Have the ssh agent running:

    ssh-agent

  To check if you have any ssh identities:

    ssh-add -l

  To add the default identities:

    ssh-add

  To remove all current identities:

    ssh-add -D

======================

A couple of things from Software Carpentry

- to get out of detached HEAD state, use "git checkout main"

- to see the files you're ignoring, use "git status --ignored"

=======================

Convert master branch to main

- on github, settings -> Branches, change default branch from master to
  main

- locally:

      git branch -m main
      git push -u origin main
      git branch -d -r origin/master

=======================

Updating git for windows, at command line:

git update-git-for-windows